Paraffin-embedded Tissue Specimens Research Articles

Identifying Genetic Mutations in Vascular Anomalies Using a Sequencing Panel for Childhood Cancers: A Pilot Study

Introduction: Genetic mutations have been identified in the pathogenesis of vascular anomalies. Due to overlaps in genetic variants causing vascular anomalies and cancer, we used a next-generation sequencing panel for genomic profiling of childhood cancers to detect somatic mutations in children with vascular anomalies. We aim to review the utility of an oncology panel for the molecular diagnosis of vascular anomalies. Methods: Nine patients with histologically confirmed vascular anomalies were included. DNA was extracted from formalin-fixed paraffin-embedded tissue specimens obtained from affected tissue following diagnostic punch biopsies of the skin and core biopsies of the vascular malformation or tumor during sclerotherapy or surgical excision. Molecular analysis of the tissue samples was performed using AmpliSeq for Childhood Cancer DNA Assay Panel. Results: Two patients had antenatally detected vascular anomalies. The median age at diagnosis for the remaining patients was 7.0 years (IQR, 0.6–10.0 years). Seven were diagnosed with vascular malformations, while 2 had vascular tumors. Pathological somatic mutations were identified in 4 patients, leading to a diagnostic yield of 44.4%. Two different PIK3CA mutations were identified in 3 cases: 1 in a case of macrocystic lymphatic malformation, the other in a case of Congenital Lipomatous Overgrowth, Vascular malformations, Epidermal nevus, Spinal/Skeletal anomalies syndrome and Klippel–Trenaunay syndrome. BRAF mutation was identified in a patient with a veno-lymphatic malformation. Conclusion: An oncology next-generation sequencing panel can be used for genetic profiling of vascular anomalies. However, a more customized and sensitive panel may be of better diagnostic yield, as detection of somatic mutations in vascular anomalies is challenging due to tissue mosaicism, low-abundant genetic variants, and specimen limitations.

Immunohistochemistry and RT-PCR as ancillary tools in the diagnosis of acquired oral syphilis.

To investigate Treponema pallidum detection using immunohistochemistry (IHC) and reverse transcription-polymerase chain reaction (RT-PCR) assays in acquired oral syphilis (AOS). Thirty-seven paraffin-embedded tissue specimens of AOS (32 secondary and five primary) were analyzed, integrating double-positive serological results with clinicodemographic and histopathological data. T. pallidum presence was semiquantitatively assessed by IHC, while RT-PCR targeted T. pallidum DNA. Sensitivity, specificity, and the area under the curve (AUC) were calculated with 95% confidence intervals (CI). The study included mostly females (62.2%) with a mean age of 27.1 years. T. pallidum was detected in all samples by IHC, predominantly in the epithelium across all layers (43.2%). RT-PCR identified T. pallidum DNA in 32 cases, with negative results observed in cases of secondary AOS. The AUC for IHC versus disease stage was 62.5% (95% CI: 45.1-77.8), and for RT-PCR, it was 57.8% (95% CI: 40.5-73.8). The AUC comparing IHC to RT-PCR was 83.8% (95% CI: 67.9-93.8). This study represents the first attempt to evaluate the proposed direct detection algorithm for AOS. IHC and RT-PCR serve as ancillary tools for detecting T. pallidum in both primary and secondary stages of AOS.

Hippo pathway effectors YAP, TAZ and TEAD are associated with EMT master regulators ZEB, Snail and with aggressive phenotype in phyllodes breast tumors

BackgroundPhyllodes tumors (PTs) of the breast are uncommon fibroepithelial neoplasms that tend to recur locally and may have metastatic potential. Their pathogenesis is poorly understood. Hippo signaling pathway plays an essential role in organ size control, tumor suppression, tissue regeneration and stem cell self-renewal. Hippo signaling dysfunction has been implicated in cancer. Recent evidence suggests that there is cross-talk between the Hippo signaling key proteins YAP/TAZ and the epithelial-mesenchymal transition (EMT) master regulators Snail and ZEB. In this study we aimed to investigate the expression of Hippo signaling pathway components and EMT regulators in PTs, in relation to tumor grade. MethodsExpression of Hippo signaling effector proteins YAP, TAZ and their DNA binding partner TEAD was evaluated by immunohistochemistry in paraffin-embedded tissue specimens from 86 human phyllodes breast tumors (45 benign, 21 borderline, 20 malignant), in comparison with tumor grade and with the expression of EMT-related transcription factors ZEB and Snail. ResultsNuclear immunopositivity for YAP, TAZ and TEAD was detected in both stromal and epithelial cells in PTs and was significantly higher in high grade tumors. Interestingly, there was a significant correlation between the expression of YAP, TAZ, TEAD and the expression of ZEB and SNAIL. ConclusionsOur results originally implicate Hippo signaling pathway in PTs pathogenesis and suggest that an interaction between Hippo signaling key components and EMT regulators may promote the malignant features of PTs.

Immunohistochemical Expression and Histopathological Role of CD47 in Colorectal Cancer in Iraqi Patients

Background: Bowel cancer is the most prevalent digestive system cancer and is the 4th largest cause of cancer-related death worldwide. In Iraq, colon and rectal cancer (CRC) is the 6th most common malignancy in males and the 5th in females. This cancer is sluggish in growth, which gives a window of opportunity to screen for both precursor lesions and early cancer. The Cluster of Differentiation 47 (CD47) protein is a type of transmembrane glycoproteins found on nearly all human cells, including non-hematopoietic and hematopoietic cells. CD47 promotes CRC growth by triggering angiogenesis and apoptosis of tumor cell. Objectives: To evaluate the immunohistochemical expression of (CD47) in various colorectal samples from Iraqi patients with CRC by immunohistochemistry (IHC) assay. Specimens and methods: A total of 45 paraffin-embedded CRC tissue specimens and clinical data were obtained from the Medical City Teaching Hospital in Baghdad and a number of private laboratories in Baghdad, Iraq. In addition, 30 control colon and rectum tissues with no significant pathology were collected from the Forensic Medicine Department for comparison purposes after taking the official approvals. Results: The results revealed a high expression of CD47 in CRC cases, but with no significant correlation with clinicopathological features. Also, the result of figures in this study revealed negative membranous expression of CD47 (score 0), strong membranous expression of CD47 (score 3), moderately membranous expression of CD47 (score 2), and weak membranous expression of CD47 (score 1) Conclusion: Patients with CRC had high CD47 expression, allowing tumor cells to modulate CD47SIRP inhibitory signaling and prevent immune cell attack.

Differential Deep RNA Sequencing for Diagnostic Detection of Microbial Infections in Inflammatory Cardiomyopathy.

Inflammatory heart disease can be triggered by a variety of causes, both infectious and noninfectious in nature. We hypothesized that inflammatory cardiomyopathy is potentially related to microbial infection. In this retrospective study, we used deep RNA sequencing on formalin-fixed paraffin-embedded heart tissue specimens to detect pathogenic agents. We first investigated 4 single-sample cases to test the feasibility of this diagnostic protocol and further 3 control-sample paired cases to improve the protocol with differential metatranscriptomics next-generation sequencing (mtNGS) analysis. We demonstrate that differential mtNGS allows identification of various microbials as potentially pathogenic, for example, Cutibacterium acnes, Corynebacterium aurimucosum, and Pseudomonas denitrificans, which are usually commensal in healthy individuals. Differential mtNGS also allows characterization of human host response in each individual by profiling alterations of gene expression, networked pathways, and inferred immune cell compositions, information of which is beneficial for us to understand different etiologies and immunity roles in each case. Additionally, differential mtNGS allows the identification of genetic variants in patients that may contribute to their susceptibility to particular microbial infections. The demonstrated power of differential mtNGS in simultaneous capture of both the infectious microbial(s) and the status of human host immune response could help us better understand the pathogenesis of complex inflammatory cardiomyopathy, if conducted on a larger scale of the population. The developed differential mtNGS method could also shed light on its translation and adoption of such a laboratory test in clinic practice, allowing for a more effective diagnosis to guide therapeutic treatment of the disease.

(042) IMMUNOSTAINING FOR MARKERS OF MAST CELLS AND NERVES IN BOTH EXCISED VESTIBULAR AND ENDOMETRIOSIS IMPLANT TISSUES IN A SINGLE PATIENT

Abstract Introduction Neuroproliferative vestibulodynia (NPV) is a chronic genital pain condition characterized by severe vestibular allodynia and hyperalgesia. The clinically suspected diagnosis of NPV is confirmed in excised vestibular tissue by immunohistochemical staining of > 8 cells per 100x magnification positively immunostained for CD 117, a mast cell marker, and 10 times the area compared to controls positively immunostained for PGP 9.5, a neuronal marker, Endometriosis, on the other hand, is a chronic pelvic pain condition associated with growth of ectopic endometrial-like tissue outside the uterus. The clinically suspected diagnosis is confirmed in excised endometriosis tissue revealing, in some patients, endometrial type glands and/or stroma. In patients with NPV and endometriosis, it is hypothesized that excess mast cells release cytokines and growth factors that promote neuroproliferation in their respective tissues, resulting in chronic genital and pelvic pain symptoms, respectively. In a study involving 65 patients with pathologically confirmed NPV, 63% reported having additional conditions associated with aberrant mast cell activity, including endometriosis. The conditions of NPV and endometriosis may both be focal to the vestibule and pelvis, respectively, but both may also share pathologies of aberrant mast cell activity with other systemic disorders. Objective To perform immunostaining for markers of mast cells and nerves in excised vestibular and endometriosis implant tissues from a single patient. Methods Fixed, paraffin-embedded vestibular tissue specimens from the 1:00-11:00 and 12:00 vestibule, and from excised endometriosis fibroadipose tissue on the rectosigmoid colon, were sectioned and immunostained for CD 117 (C-kit) and PGP 9.5. The immunostained slides were examined and digital photomicrographs taken. A minimum of 2 photomicrographs were examined at 100x magnification for each stained slide, identifying representative regions of the excised tissue. Manual counting of CD117 and PGP 9.5 immunopositive profiles, cells/nerves per 100x magnification, was performed for each photomicrograph. Results A 23-year-old woman presented with a history marked by painful and prolonged menstrual periods, inability to insert tampons, and discomfort with both entry and deep thrusting during intercourse. After excluding other forms of vestibulodynia, she underwent complete 1:00-11:00 and 12:00 subepithelial vestibulectomy with vaginal advancement flap reconstruction. Post-operatively, she reported “very much better” symptoms, with a reduction of entrance dyspareunia, but continued to experience deep thrusting pain with penetrative sexual activity. She subsequently underwent endometriosis excision surgery with positive lesions identified in 12 locations in the pelvis and retroperitoneum. Tissue stained for CD117 and PGP9.5 analyzed by manual counting exhibited > 20 immunopositive cells and nerves per 100x microscopic field in the epithelial basement membrane and adjacent subepithelial regions of the 1:00-11:00 and 12:00 vestibule, as well as in the endometriosis fibroadipose tissue on the rectosigmoid colon. Conclusions We report for the first time, in a single patient diagnosed with both NPV and endometriosis, immunostaining findings of high densities of mast cells and nerves in their respective tissues. These findings reinforce the hypothesis that NPV and endometriosis are linked to a broader condition associated with aberrant mast cell activity. Disclosure No.

Age-dependent increase of perineuronal nets in the human hippocampus and precocious aging in epilepsy.

Perineuronal nets (PNN) are specialized extracellular matrix (ECM) components of the central nervous system, frequently accumulating at the surface of inhibitory GABAergic interneurons. While an altered distribution of PNN has been observed in neurological disorders including Alzheimer's disease, schizophrenia and epilepsy, their anatomical distribution also changes during physiological brain maturation and aging. Such an age-dependent shift was experimentally associated also with hippocampal engram formation during brain maturation. Our aim was to histopathologically assess PNN in the hippocampus of adult and pediatric patients with temporal lobe epilepsy (TLE) compared to age-matched post-mortem control subjects and to compare PNN-related changes with memory impairment observed in our patient cohort. Sixty-six formalin-fixed and paraffin-embedded tissue specimens of the human hippocampus were retrieved from the European Epilepsy Brain Bank. Twenty-nine patients had histopathologically confirmed hippocampal sclerosis (HS), and eleven patients suffered from TLE without HS. PNN were immunohistochemically visualized using an antibody directed against aggrecan and manually counted from hippocampus subfields and the subiculum. PNN density increased with age in both human controls and TLE patients. However, their density was significantly higher in all HS patients compared to age-matched controls. Intriguingly, TLE patients presented presurgically with better memory when their hippocampal PNN density was higher (p < 0.05). Our results were compatible with age-dependent ECM specialization in the human hippocampus and its precocious aging in the epileptic condition. These observations confirm recent experimental animal models and also support the notion that PNN play a role in memory formation in the human brain. "Perineuronal nets" (PNN) are a specialized compartment of the extracellular matrix (ECM), especially surrounding highly active neurons of the mammalian brain. There is evidence that PNN play a role in memory formation, brain maturation, and in some pathologies like Alzheimer's disease, schizophrenia or epilepsy. In this study, we investigated the role of PNN in patients suffering from drug-resistant focal epilepsy compared to controls. We found that with increasing age, more neurons are surrounded by PNN. Similarly, all epilepsy patients but especially patients with better memory performance also had more PNN. This study raises further interest in studying ECM molecules in the human brain under physiological and pathophysiological conditions.

Multinational, Multicenter Evaluation of Prostate Cancer Tissue in Sub-Saharan Africa: Challenges and Opportunities.

Prostate cancer disproportionately affects men of African descent, yet their representation in tissue-based studies is limited. This multinational, multicenter pilot study aims to establish the groundwork for collaborative research on prostate cancer in sub-Saharan Africa. The Men of African Descent and Carcinoma of the Prostate network formed a pathologist working group representing eight institutions in five African countries. Formalin-fixed paraffin-embedded prostate tissue specimens were collected from Senegal, Nigeria, and Ghana. Histology slides were produced and digitally scanned. A central genitourinary pathologist (P.L.) and eight African general pathologists reviewed anonymized digital whole-slide images for International Society of Urological Pathology grade groups and other pathologic parameters. Discrepancies were re-evaluated, and consensus grading was assigned. A virtual training seminar on prostate cancer grading was followed by a second assessment on a subcohort of the same tissue set. Of 134 tissue blocks, 133 had evaluable tissue; 13 lacked cancer evidence, and four were of insufficient quality. Post-training, interobserver agreement for grade groups improved to 56%, with a median Cohen's quadratic weighted kappa of 0.83 (mean, 0.74), compared with an initial 46% agreement and a quadratic weighted kappa of 0.77. Interobserver agreement between African pathologist groups was 40%, with a quadratic weighted kappa of 0.66 (95% CI, 0.51 to 0.76). African pathologists tended to overgrade (36%) more frequently than undergrade (18%) compared with the reference genitourinary pathologist. Interobserver variability tended to worsen with a decrease in tissue quality. Tissue-based studies on prostate cancer in men of African descent are essential for a better understanding of this common disease. Standardized tissue handling protocols are crucial to ensure good tissue quality and data. The use of digital slide imaging can enhance collaboration among pathologists in multinational, multicenter studies.

Association of overexpression of TNF receptor superfamily members (CD40, BAFFR, LTβR and RANK) with favorable prognosis in patients with colorectal adenocarcinoma.

e15516 Background: Numerous studies by our and other groups have highlighted the implication of NF-κB in colorectal cancer (CRC) through the deterioration of classical and alternative pathway signaling. The alternative pathway of NF-κB can be activated by members of TNF superfamily, such as lymphotoxin β (LTβ), tumor necrosis factor ligand superfamily member 5 (CD40L), B-cell activation factor (BAFF) and receptor activator of NF-κB ligand (RANKL). We have previously shown that alternative pathway of NF-κΒ is deteriorated in CRC. In the present study, we investigated the clinical significance of the aforementioned receptors in patients with CRC as well as their relation with effector transcription factors NF-κB2 and RELB. Methods: Gene expression of CD40, BAFFR, LT β R, RANK, NF- κ B2 and RELB, quantified by using real-time qRT-PCT and specific primers and probes, was assessed in 97 cancerous and 61 paired non-neoplastic tumor-adjacent formalin-fixed paraffin-embedded (FFPE) tissue specimens from CRC patients who were surgically managed in the University Hospital of Patras, Greece. Concurrently, we assessed protein expression of the same molecules by immunohistochemistry in the same cohort of patients. Both, mRNA and protein levels of the receptors were analyzed in association with clinicopathological parameters and clinical outcome of the patients in terms of time to disease progression. Results: Cytoplasmic expression of all molecules was higher in cancer compared to tumor-adjacent epithelial cells ( p= 0.047 for CD40, p= 0.007 for BAFFR, p&lt; 0.001 for LTβR and p= 0.003 for RANK) and in stromal cells ( p&lt; 0.001 for all molecules), while the reverse pattern (lower in neoplastic epithelial cells) was observed for nuclear expression ( p&lt; 0.001 for all molecules). Similarly, mRNA levels of LTβR and RANK were higher in cancer compared to adjacent non-neoplastic tissues ( p= 0.019 and p= 0.037, respectively). Notably, patients with high mRNA levels of all studied receptors had significantly longer time to disease progression ( p= 0.026 for CD40, p= 0.023 for BAFFR, p= 0.027 for LTβR and p= 0.038 for RANK). In addition, mRNA levels of BAFFR, LTβR and RANK levels were higher in ulcerative tumors compared to polypoid tumors ( p= 0.002, p= 0.005 and p= 0.011, respectively). RELB mRNA levels were positively correlated with mRNA levels of CD40, BAFFR and LTβR in cancerous ( p&lt; 0.001 for all molecules) and non-cancerous tissues (p &lt; 0.001 for all molecules). Surprisingly, NF-κB2 mRNA levels were positively correlated with BAFFR and LTβR mRNA levels in malignant tissues, while in non-malignant tissues were positively correlated with all receptors’ mRNA levels ( p&lt; 0.001 for all molecules). Conclusions: This study suggests a prognostic value for CD40, BAFFR, LTβR and RANK expression in patients with CRC and further supports the role of the alternative pathway of NF-κB in CRC.

Abstract A007: Circulating tumor DNA and tissue staining analyses reveal heterogeneous ERBB2/HER2 status in urothelial cancer

Abstract Human epidermal growth factor receptor 2 (HER2) is encoded by the ERBB2 gene, and frequently mutated, amplified, and/or overexpressed in urothelial cancer (UC). Promising antibody-drug conjugates have led to new interest in HER2 as a UC clinical target. Patient selection for HER2-targeted therapy typically relies on immunohistochemistry (IHC) and fluorescence in-situ hybridization (FISH) of tumor tissue, however DNA sequencing can identify ERBB2 genomic alterations. Accurate biomarker-driven patient selection will be critical to optimize the clinical benefit of HER2-targeted therapy. Therefore, we evaluated plasma circulating tumor DNA (ctDNA) for ERBB2/HER2 status determination in UC, as compared to IHC and FISH of metachronous tissue. 411 plasma samples from 236 metastatic UC patients were profiled with targeted sequencing across &amp;gt;50 genes frequently altered in UC, including dense coverage flanking the ERBB2 locus. Using an established bioinformatics workflow, we determined the presence of ERBB2 alterations (mutations, amplifications, and/or structural variants) in the 181 patients with evidence of ctDNA in ≥1 sample. Clinical records were reviewed for the availability of archival tumor tissue; in total, 81 formalin-fixed paraffin-embedded tissue specimens were retrieved from 23 patients with ctDNA ERBB2 alterations and 20 ERBB2-wildtype controls. HER2 IHC was performed with a polyclonal rabbit anti-human Her2 antibody (Dako) and scored according to gastric cancer guidelines. HER2 FISH was performed with the PathVysion HER-2 DNA Probe Kit. Protein-altering ERBB2 mutations were identified in 14% of evaluable patients, with two-thirds at known oncogenic hotspots. ERBB2 copy gain was detected in 8% of patients overall, 9% when excluding low tumor fraction samples. IHC results were assessable for 82 tissue samples from 43 patients, and 33 patients had at least one sample with positive HER2 staining (2+/3+). IHC scores varied in 16/23 patients with ≥2 tissue samples, with the variation leading to a change in classification (HER2-negative [0/1+] versus positive [2+/3+]) in half (8/16). In two patients with mixed variant histology, the urothelial component showed IHC 3+ while the scores were 2+ (plasmacytoid) and 0 (squamous) in the variant regions. Frequent focal staining patterns were observed with both IHC and FISH. ERBB2 alterations in ctDNA were correlated with IHC positivity – when considering the most recent tissue sample per patient, 79% of ctDNA ERBB2-altered patient’s tumors were also positive by IHC. Conversely, 55% of ctDNA ERBB2-wildtype cases were positive by IHC. FISH results were available from 24 samples (20 positive, 4 negative), all from patients with ctDNA ERBB2 amplification. 18/20 samples with FISH positivity were HER2 IHC 2+/3+; the remaining two samples were IHC 1+. Our results demonstrate significant spatial and/or temporal heterogeneity in ERBB2/HER2 status, with implications for the rational implementation of biomarker-directed (HER2-targeted) therapy in UC. Citation Format: Gillian Vandekerkhove, Andrew J. Murtha, David C. Müller, Kimia Rostin, Carlos Vasquez-Rios, Jussi Nikkola, Maria Stephenson, Emily Fung, Jaskirat Atwal, Karan Parekh, Cecily Q. Bernales, Gráinne Donnellan, Gang Wang, Tilman Todenhöfer, Piet Ost, Peter C. Black, Kim N. Chi, Bernhard J. Eigl, Alexander W. Wyatt. Circulating tumor DNA and tissue staining analyses reveal heterogeneous ERBB2/HER2 status in urothelial cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr A007.

Profiling of microRNAs by next-generation sequencing: Potential biomarkers for diffuse large B-cell lymphoma

BackgroundLymphoma ranks fifth in prevalence among common cancer types worldwide. This lymphatic system cancer arises from T or B cells. Diffuse large B cell lymphomas (DLBCLs) are associated with most non-Hodgkin lymphomas. Non-coding microRNAs (miRNAs) greatly affect gene expression. A single miRNA can target numerous genes, thus largely influencing gene expression networks. MiRNAs can act as oncogenes or tumor suppressors in controlling DLBCL progression. This study investigated the roles of miRNAs in patients with DLBCL through next-generation sequencing, which was found to be sensitive, accurate, and robust. MethodsThe study involved seven patients with DLBCLs and three controls at a hematology-oncology clinic. MiRNA was extracted from existing formalin-fixed, paraffin-embedded (FFPE) tissue specimens. Illumina next-generation sequencing was used to sequence samples for miRNA profiling. ResultsSamples from patients showed expression of various hsa-mir miRNAs (1248, 3607, 21, 142, 1244, 182, 6516, 766, 1291, 4449, and 181a), whereas those from healthy individuals showed expression of hsa-mir 1248, 3607, 21, 142, and 877. Hsa-mir-877-3p is known to target multiple genes, and miRNAs such as hsa-mir-877-3p, hsa-mir-1291, and hsa-mir-181a-5p interact primarily with target genes. ConclusionsMiRNA profiling in FFPE tissues from patients with DLBCL suggested that miRNA levels can distinguish patients with DLBCL from controls, and therefore may provide prognostic or diagnostic biomarkers for DLBCL. Altered genes and miRNAs may also be potential therapeutic targets.

Granulomatous lymphadenitis in Taiwan: Unraveling infantile peak and Bacillus Calmette-Guérin lymphadenitis

BackgroundGranulomatous lymphadenitis, a histopathological diagnosis, often indicates infections, such as those caused by mycobacterial and fungal agents. MethodsWe conducted an analysis of 1098 granulomatous lymphadenitis cases, examining age distribution, lymph node locations, and laterality. Molecular detection of Bacillus Calmette-Guérin (BCG) was performed on archived formalin-fixed paraffin-embedded tissue specimens. ResultsOur analysis revealed a bimodal age distribution, notably with a minor peak in infants. These infantile cases predominantly featured axillary involvement, frequently occurring on the left side. Positive rates of BCG identification decreased with age: <1 year, 71%; 1–2 year, 33%; 2–3 year, 13%; 3–4 year, 0%. Remarkably, only one of the 14 cases with molecularly confirmed BCG lymphadenitis had comments regarding BCG in the pathological report. Compared with patients born after 2016 (BCG at 5–8 months), those born before 2016 (BCG at birth) developed BCG lymphadenitis at a wider age range with right skewness (before 2016, 13 ± 11 months [range, 3–33 months] vs. after 2016, 10 ± 2 months [range, 8–13 months]). Four of the 14 BCG-positive cases had congenital heart disease. Seven patients received anti-tuberculosis drugs following surgical excision. No surgical complications were reported. ConclusionsBCG lymphadenitis constitutes a distinctive minor peak within the spectrum of granulomatous lymphadenitis in Taiwan. Pathologists should consider the possibility of BCG infection, especially in cases of infantile axillary, supraclavicular, neck lymphadenopathies on the left side. Moreover, BCG administration at 5–8 months may reduce delayed-onset BCG lymphadenitis.

CORRELATION OF TUMOR MARKERS HER2 NEU ER PR AND KI 67 IN BREAST CANCER PATIENTS

: Every year, more than a million women are diagnosed with breast cancer, and over 700.000 of them have positive for hormone receptors (FIR). The expression of key markers, such as ER and PP, and clinical circumstances show specific biological traits. Risk factors may have a role in the development of some hormone receptor-positive breast cancers. Objective: The objective of this study was to investigate the correlations between key tumor markers, including HER2, ER, PR, ALP, and KI67, in hormone receptor-positive breast cancers. Methods: Tumour tissue samples were collected for histopathology (10% neutral buffered Formalin-fixed paraffin-embedded tissue specimens) during Trucut biopsy or mastectomy at the oncology department of a tertiary care hospital in Karachi from October 2022 to July 2023. Tissues were analyzed under a light microscope for tumor hormone receptors at a tertiary care hospital in Karachi. Results: There were several significant correlations observed between HER 2 NUE, KI 67, ER, and PR. Specifically, a weak negative correlation was noted between HER 2 NUE and KI 67, while weak positive correlations were observed between HER 2 NUE and both ER and PR. Additionally, a weak positive correlation was found between ER and HER 2 NUE, PR, and KI 67, and a weak positive correlation existed between PR and ER, HER 2 NUE, and KI 67. Finally, KI 67 displayed a weak positive correlation with HER 2 NUE, PR, and ER. Conclusions: Her two nurses, ER, ALP, KI 67, and breastfeeding, are significantly and directly related. PR is not significantly related to other mentioned tumor markers.

Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues.

Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.

Abstract 2275: Reducing artifactual somatic variant calls from formalin-fixed paraffin-embedded specimens by using DEEPOMICS FFPE, a bioinformatic approach based on deep neural networks

Abstract Formalin-fixed, paraffin-embedded (FFPE) tissue specimens are routinely used in pathological diagnosis. However, formalin induced artificial mutations make it challenging to accurately analyze next-generation sequencing data. Existing FFPE filtering tools tend to categorize all low-frequency variants as artifacts, making it difficult to identify true variants with low allele frequencies, compromising analysis of tumors with low tumor cell content. To address this issue, we developed DEEPOMICS FFPE, an AI model designed to distinguish true variants from artifacts. We gathered paired exome genome sequencing data from both fresh frozen and FFPE samples of 24 tumors from public sources. These data were used to train and validate the model, with a split of 70% for training and 30% for validation. The deep neural network model, comprising three hidden layers, was trained using input features derived from the outputs of the MuTect2 caller. We employed the SHapley Additive exPlanations algorithm to identify relevant features, and then fine-tuned them based on the training outcomes. We assessed the performance of the final DEEPOMICS FFPE model in comparison to existing models (MuTect filter, FFPolish, and SOBDetector) using well-defined test datasets. Our findings revealed 43 distinguishing characteristics for FFPE artifacts. Refining the quantification of these characteristics resulted in improved model performance. DEEPOMICS FFPE successfully filtered out 99.6% of artifacts while retaining 85.2% of true variants, achieving an F1-score of 87.8 in the validation dataset, surpassing the performance of existing tools. Furthermore, the model demonstrated consistent performance even for variants with low allele frequencies, exhibiting a specificity of 0.998, suggesting its capability to identify subclonal variants. Future enhancement of the model will include the ability to use other variant callers and analysis of whole genome sequencing data. This newly developed tool has potential applications in designing capture panels for personalized circulating tumor DNA assays and identifying candidate neoepitopes for personalized vaccine development. DEEPOMICS FFPE is freely accessible for research purposes on the web at http://deepomics.co.kr/ffpe. Citation Format: Dong-hyuk Heo, Inyoung Kim, Heejae Seo, Seong-Gwang Kim, Minji Kim, Jiin Park, Hongsil Park, Seungmo Kang, Juhee Kim, Soonmyung Paik, Seong-Eui Hong. Reducing artifactual somatic variant calls from formalin-fixed paraffin-embedded specimens by using DEEPOMICS FFPE, a bioinformatic approach based on deep neural networks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2275.

Abstract 2266: Detection of androgen receptor splice variants from clinical sequencing

Abstract Background: Androgen receptor splice variant-7 (AR-v7) has been widely studied as a biomarker of resistance to AR-targeted therapy in castration-resistant prostate cancer (CRPC). Various methods have been used to detect AR-v7 in CRPC specimens, including next generation sequencing (NGS) technology. However, NGS technologies applied in clinical sequencing have focused on using blood or fresh-frozen CRPC tissue specimens. There is not yet an AR-v7 detection system tailored to formalin-fixed paraffin-embedded (FFPE) tissue specimens commonly used for clinical sequencing in hospitals. Methods: In this respect, we propose a novel approach to identify AR-v7 in targeted RNA sequencing (RNA-seq) data derived from FFPE specimens. This approach can identify, in addition to AR-v7, all constitutively active AR splice variants (AR-Vs) that are co-expressed with AR-v7. In short, our two-step approach first gathers soft-clipped or divided reads that are adjacent to the splicing sites of AR-Vs and then yields the number of splitting reads that support the existence of AR-Vs. Next, the algorithm selects the paired-end reads whose one side and the other side are mapped to the preceding and following exons, respectively. The final number of spanning reads are calculated following to the removal of low-quality reads. Results: We validated the proposed approach using two large-scale, independent RNA-seq datasets of prostate cancer (PC) samples: 111 samples from Seoul National University Hospital (SNUH) and 558 samples from The Cancer Genome Atlas (TCGA) dataset. The majority of both datasets were localized PC tumors, especially in the SNUH dataset, where localized PC accounted for 91% of the total. Overall, our approach successfully identified samples with putative AR-Vs, including AR-v7, AR-v3, and AR-v9. Statistical analyses of 111 SNUH PC patients suggested potential detection threshold in clinical sequencing settings (at least 200 split reads). In the SNUH dataset, the AR-v7 positive group, which included 5 patients (5%) with values above the threshold, shared the following characteristics: higher AR-v7/full length AR expression levels, AR amplification and co-expression with AR-v3/AR-v9. AR-v7 positivity was experimentally validated by Sanger sequencing. The similar pattern was also found in the analysis of TCGA dataset. Conclusions: These results demonstrate that the detection system can successfully identify AR-v7 positivity not only for metastatic PC but also for patients with localized PC through clinical sequencing. We expect that the further in-depth analyses including larger samples and clinical outcomes can discover clinical applicability of AR-v7. Citation Format: Suhyun Hwangbo, Sungyoung Lee, Sheehyun Kim, Hongseok Yun. Detection of androgen receptor splice variants from clinical sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2266.

Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing.

In the molecular era, proper archival conditions within pathology laboratories are crucial, especially for formalin-fixed paraffin-embedded (FFPE) tissue specimens retrieved years after the original diagnosis. Indeed, improper preservation can impact the integrity of nucleic acids and protein antigens. This study evaluates the quality status of stored FFPE blocks using multilevel omics approaches. FFPE blocks from 45 Non-Small Cell Lung Carcinoma (NSCLC) cases were analyzed. The blocks were collected from six different pathology archives across Italy with distinct environmental characteristics. Nucleic acids' quantity and quality, as well as protein antigens, were assessed using various techniques, including MALDI-MSI. RNA was quantitatively higher, but more fragmented, compared to DNA. DNA quantity and quality were suitable for molecular analyses in 94.4% and 62.3% of samples, respectively. RNA quantity was adequate across all samples, but it was optimal only in 22.3% of cases. DNA quality started to deteriorate after 6-8 years, whereas RNA quality diminished only after 10 years of storage. These data might suggest a particular DNA susceptibility to FFPE blocks conservation. Immunohistochemical intensity decreased significantly after 6-8 years of storage, and MALDI-MSI analysis revealed that younger tissue blocks contained more unique proteomic signals than the older ones. This study emphasizes the importance of proper FFPE archiving conditions for molecular analyses. Governance should prioritize attention to pathology archives to ensure quality preservation and optimize predictive testing. By elucidating the nuances of FFPE block storage, this research paves the way for enhanced molecular diagnostics and therapeutic insights regarding oncology and beyond.

Abstract 7005: Distinct DNA methylation patterns between early-onset and average-onset colorectal cancer patients

Abstract Objective: Early onset colorectal cancer (EO CRC) is rising at an alarming rate. While average onset colorectal cancer (AO CRC) affects patients mostly above 65 years of age, EO CRC affects patients under 50 years of age, disproportionately affecting males from low-income communities and racial/ethnic minorities. Chronic inflammation has been identified as a strong contributor to pathogenesis. We hypothesize that methylation of DNA may serve as a potential mechanism associated with chronic inflammation that contributes to the etiology differentially between EO and AO CRC. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue specimens from four AO and EO CRC patients each were retrieved from the Tissue Repository. Paraffin curls containing tumor and adjacent normal tissues were generated from appropriate EO and AO CRC patient tissues. The Qiagen GeneRead DNA FFPE genomic DNA kit was then used to extract the DNA from the paraffin curls. Illumina Methylation EPIC v2.0 kit was used to evaluate DNA methylation (DNAm) patterns after the restoration process from deamination in the fixed/embedded sample using the Uracil-N-Glycosylase enzyme. Unreliable and non-specific probes were removed before statistical analysis for differentially methylated CpG sites. Age acceleration for each tissue was calculated by comparing the estimated DNAm age with chronological age using the Horvath approach. Results: A clear clustering of DNAm patterns by age of onset were observed for both normal and tumor tissues. However, there was no difference when comparing tumor and normal tissues after multiple corrections. Four-way ANCOVA adjusting for race, gender, BMI, and tissue type suggested that age onset was the most significant factor. We also found that age acceleration in EO CRC tissue is greater than in AO CRC. After applying Bonferroni correction, significant differentially methylated regions (DMRs) were found in the promoter and the gene body of SNTB1, NFATC3, SLC25A24, RABGAP1L, WDSUB1, WWOX, SELB, SLC28A3, and PPP6R2 in EO CRC patients when compared to AO CRC. SNTB1 regulates colorectal cancer progression and stemness, while NFATC3 has been associated with inflammation and cancer. Conclusions: The preliminary results from this study showed a significant difference in the DNAm profile of FFPE samples between AO and EO CRC. The finding suggests that epigenetics may play a role in the etiology of CRC, potentially involved in the chronic inflammation pathway. The analysis of a larger patient number is underway to strengthen these findings. Citation Format: L. Joseph Su, Ping-Ching Hsu, Aniruddha Rathod, Yulun Liu, Jacopo Ferruzzi, Syed Kazmi, Emina Huang. Distinct DNA methylation patterns between early-onset and average-onset colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7005.

Predominance of T-bet-positive Th1 cells in infiltrating T-lymphocytes in most of active arteritis lesions of giant cell arteritis.

Immunological mechanisms through the activation of CD4-positive T-cells have been assumed to be involved in the pathogenesis of giant cell arteritis (GCA). Many studies employing frozen tissues of temporal artery biopsy, peripheral blood lymphocytes, and plasma of GCA patients have revealed the contribution of interferon-γ and interleukin-17 in both protein and mRNA levels. However, the analyses using formalin-fixed and paraffin-embedded (FFPE) tissue specimens, in which the correlation between histopathologic pictures and immunological circumstances would be elucidated, have been limited. Here, we performed the immunohistochemical analyses of infiltrating small lymphocytes in GCA lesions using FFPE specimens, especially of the subsets of CD4-positive T-cells by immunohistochemistry with antibodies against T-bet, GATA-3, RORγT, and Foxp3, which is the differentiation-specific transcription factor for Th1, Th2, Th17, and Treg cells, respectively. In these slides, the nuclear-positive staining is much more clearly and easily identifiable than the cytoplasmic staining for cytokines. The results indicate the predominance of T-bet-positive Th1 cells in infiltrating T-cells in most of active arteritis lesions of GCA. Furthermore, our data suggest the possible immunosuppressive microenvironment induced by T-reg cells and M2-type macrophages in the arteritis lesions throughout the course of GCA inflammation.

Abstract A063: What can we learn from a retrospective evaluation of HER2, P53 and P16INK4A protein expression in rare ovarian tumors?

Abstract A063: What can we learn from a retrospective evaluation of HER2, P53 and P16INK4A protein expression in rare ovarian tumors?